Custom post types such as portfolio, sponsors, gallery, quotes and so on all must have the taxonomy and slug defined in their post type when the theme is created. This creates a URL structure that allows the templates to properly link to posts of its own post type. For example http://www.yoursite.com/portfolio/portfolio-category/portfolio-post-title

You can easily hide the slug by downloading and activating the Remove Slug from Custom Post Type plugin under Plugins > Add New, or with an SEO plugin such as WordPress SEO. Note that this plugin may not work if you are using subdomains, or have WordPress installed in a sub-folder. You can also attempt to setup a custom permalink structure under Setttings > Permalinks if you are using WooCommerce.

Changing the slug inherently in the theme is a very long and complex process that should not be attempted unless you are familiar with PHP and WordPress development.To do so, you will need an hTML editor such as Dreamweaver to find and replace all instances of the slug with your desired slug.  The slug cannot be the same as the post type name or a reserved WordPress slug. See the following for details:

http://codex.wordpress.org/Function_Reference/register_post_type

You will also need to change any corresponding template file names.